Re: [modeller_usage] Problems with mod8v1

[Modeller Caretaker <>]

Elza Helena Andrade Barbosa wrote:
> I made a theoretical model in modeller7v7 and now, when I try to do it
> again in modeller8v1, I get the following error:

This error occurs because you have both the INCLUDE command (which 
defines Modeller variables and routines) and the various DEFINE_STRING, 
DEFINE_INTEGER, and DEFINE_REAL commands (which define the variables). 
This means that you've tried to define every variable twice, which 
results in undefined behavior (I guess you got lucky and it worked with 
7v7).

Two possible solutions:
1. Remove the DEFINE_INTEGER, DEFINE_REAL, and DEFINE_STRING commands 
from the start of your TOP file. They're redundant anyway, since the 
INCLUDE does all of this.

2. Apply the attached patch to your 8v1 installation, which will allow 
you to redefine variables in the same manner as in 7v7.

	Ben Webb, Modeller Caretaker
--
             http://www.salilab.org/modeller/
Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage

Index: modlib/modeller/runtop.py
===================================================================
--- modlib/modeller/runtop.py	(revision 2848)
+++ modlib/modeller/runtop.py	(working copy)
@@ -248,7 +248,8 @@
         raise IndexError, "No '=' found in variable assignment"
       varname = var[:ind].strip().lower()
       varval = var[ind+1:].strip()
-      varval = self.parse_var(varval, varname!='result')
+      varval = self.parse_var(varval,
+                              varname!='result' and varname!='variables')
       if varname in self.variables:
         self.variables[varname] = varval
       else: